A nonparametric ensemble transform method for Bayesian inference

Many applications, such as intermittent data assimilation, lead to a recursive application of Bayesian inference within a Monte Carlo context. Popular data assimilation algorithms include sequential Monte Carlo methods and ensemble Kalman filters (EnKFs). These methods differ in the way Bayesian inference is implemented. Sequential Monte Carlo methods rely on importance sampling combined with a resampling step, while EnKFs utilize a linear transformation of Monte Carlo samples based on the classic Kalman filter. While EnKFs have proven to be quite robust even for small ensemble sizes, they are not consistent since their derivation relies on a linear regression ansatz. In this paper, we propose another transform method, which does not rely on any a priori assumptions on the underlying prior and posterior distributions. The new method is based on solving an optimal transportation problem for discrete random variables. © 2013, Society for Industrial and Applied Mathematics

Ensemble transform Kalman-Bucy filters

Two recent works have adapted the Kalman–Bucy filter into an ensemble setting. In the first formulation, the ensemble of perturbations is updated by the solution of an ordinary differential equation (ODE) in pseudo-time, while the mean is updated as in the standard Kalman filter. In the second formulation, the full ensemble is updated in the analysis step as the solution of single set of ODEs in pseudo-time. Neither requires matrix inversions except for the frequently diagonal observation error covariance. We analyse the behaviour of the ODEs involved in these formulations. We demonstrate that they stiffen for large magnitudes of the ratio of background error to observational error variance, and that using the integration scheme proposed in both formulations can lead to failure. A numerical integration scheme that is both stable and is not computationally expensive is proposed. We develop transform-based alternatives for these Bucy-type approaches so that the integrations are computed in ensemble space where the variables are weights (of dimension equal to the ensemble size) rather than model variables. Finally, the performance of our ensemble transform Kalman–Bucy implementations is evaluated using three models: the 3-variable Lorenz 1963 model, the 40-variable Lorenz 1996 model, and a medium complexity atmospheric general circulation model known as SPEEDY. The results from all three models are encouraging and warrant further exploration of these assimilation techniques.

Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits

The environmental and financial costs of using inorganic phosphate fertilizers to maintain crop yield and quality are high. Breeding crops that acquire and use phosphorus (P) more efficiently could reduce these costs. The variation in shoot P concentration (shoot-P) and various measures of P use efficiency (PUE) were quantified among 355 Brassica oleracea L. accessions, 74 current commercial cultivars, and 90 doubled haploid (DH) mapping lines from a reference genetic mapping population. Accessions were grown at two or more external P concentrations in glasshouse experiments; commercial and DH accessions were also grown in replicated field experiments. Within the substantial species-wide diversity observed for shoot-P and various measures of PUE in B. oleracea, current commercial cultivars have greater PUE than would be expected by chance. This may be a consequence of breeding for increased yield, which is a significant component of most measures of PUE, or early establishment. Root development and architecture correlate with PUE; in particular, lateral root number, length, and growth rate. Significant quantitative trait loci associated with shoot-P and PUE occur on chromosomes C3 and C7. These data provide information to initiate breeding programmes to improve PUE in B. oleracea.

A benchmark-driven modelling approach for evaluating deployment choices on a multicore architecture

The complexity of current and emerging high performance architectures provides users with options about how best to use the available resources, but makes predicting performance challenging. In this work a benchmark-driven performance modelling approach is outlined that is appro- priate for modern multicore architectures. The approach is demonstrated by constructing a model of a simple shallow water code on a Cray XE6 system, from application-specific benchmarks that illustrate precisely how architectural char- acteristics impact performance. The model is found to recre- ate observed scaling behaviour up to 16K cores, and used to predict optimal rank-core affinity strategies, exemplifying the type of problem such a model can be used for.

Architectural enthusiasm: visiting buildings with The Twentieth Century Society

In this paper we put forward the concept of architectural enthusiasm—a collective passion and shared emotional affiliation for buildings and architecture. Through this concept and empirical material based on participation in the architectural tours of The Twentieth Century Society (a UK-based architectural conservation group), we contribute to recent work on the built environment and geographies of architecture in three ways: first, we reinforce the importance of emotion to people’s engagements with buildings, emphasising the shared and practised nature of these engagements; second, we highlight the role of architectural enthusiasts as agents with the potential to shape and transform the built environment; and third, we make connections between (seemingly) disparate engagements with buildings through a continuum of practice incorporating urbex, local history, architectural practice and training, and mass architectural tourism. Unveiling these continuities has important implications for future research into the built environment, highlighting the need to take emotion seriously in all sorts of professional as well as enthusiastic encounters with buildings, and unsettling the categories of amateur and expert within architectural practices.

Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample

The self-assembly of proteins and peptides into b-sheet-rich amyloid fibers is a process that has gained notoriety because of its association with human diseases and disorders. Spontaneous self-assembly of peptides into nonfibrillar supramolecular structures can also provide a versatile and convenient mechanism for the bottom-up design of biocompatible materials with functional properties favoring a wide range of practical applications.[1] One subset of these fascinating and potentially useful nanoscale constructions are the peptide nanotubes, elongated cylindrical structures with a hollow center bounded by a thin wall of peptide molecules.[2] A formidable challenge in optimizing and harnessing the properties of nanotube assemblies is to gain atomistic insight into their architecture, and to elucidate precisely how the tubular morphology is constructed from the peptide building blocks. Some of these fine details have been elucidated recently with the use of magic-angle-spinning (MAS) solidstate NMR (SSNMR) spectroscopy.[3] MAS SSNMR measurements of chemical shifts and through-space interatomic distances provide constraints on peptide conformation (e.g., b-strands and turns) and quaternary packing. We describe here a new application of a straightforward SSNMR technique which, when combined with FTIR spectroscopy, reports quantitatively on the orientation of the peptide molecules within the nanotube structure, thereby providing an additional structural constraint not accessible to MAS SSNMR.

GridRM: a resource monitoring architecture for the grid

Monitoring resources is an important aspect of the overall efficient usage and control of any distributed system. In this paper, we describe a generic open-source resource monitoring architecture that has been specifically designed for the Grid. The paper consists of three main sections. In the first section, we outline our motivation and briefly detail similar work in the area. In the second section, we describe the general monitoring architecture and its components. In the final section of the paper, we summarise the experiences so far and outline our future work.

Bioactive films produced from self-assembling peptide amphiphiles as versatile substrates for tuning cell adhesion and tissue architecture in serum-free conditions

The development of versatile bioactive surfaces able to emulate in vivo conditions is of enormous importance to the future of cell and tissue therapy. Tuning cell behaviour on two-dimensional surfaces so that the cells perform as if they were in a natural three-dimensional tissue represents a significant challenge, but one that must be met if the early promise of cell and tissue therapy is to be fully realised. Due to the inherent complexities involved in the manufacture of biomimetic three-dimensional substrates, the scaling up of engineered tissue-based therapies may be simpler if based upon proven two-dimensional culture systems. In this work, we developed new coating materials composed of the self-assembling peptide amphiphiles (PAs) C16G3RGD (RGD) and C16G3RGDS (RGDS) shown to control cell adhesion and tissue architecture while avoiding the use of serum. When mixed with the C16ETTES diluent PA at 13 : 87 (mol mol-1) ratio at 1.25 times 10-3 M, the bioactive {PAs} were shown to support optimal adhesion, maximal proliferation, and prolonged viability of human corneal stromal fibroblasts ({hCSFs)}, while improving the cell phenotype. These {PAs} also provided stable adhesive coatings on highly-hydrophobic surfaces composed of striated polytetrafluoroethylene ({PTFE)}, significantly enhancing proliferation of aligned cells and increasing the complexity of the produced tissue. The thickness and structure of this highly-organised tissue were similar to those observed in vivo, comprising aligned newly-deposited extracellular matrix. As such, the developed coatings can constitute a versatile biomaterial for applications in cell biology, tissue engineering, and regenerative medicine requiring serum-free conditions.

Information architecture for healthcare organizations: the case of a NHS Hospital in UK

Healthcare organizations are known for their complex and intense information environment. Healthcare information is facilitated via heterogeneous information systems or paper-based sources. Access to the right information under increasing time pressure is extremely challenging. This paper proposes an information architecture for healthcare organizations. It facilitates the provision of the right information to the right person in the right place and time tailored to their requirements. It adapts an abductive reasoning research approach. Organizational semiotics serves as its theoretical underpinning, guiding the data collection process through direct observation in the ophthalmology outpatient clinics of a UK hospital. It results the norm and information objects that form the information architecture. This is modeled by Archimate. The contribution of the information architecture can be seen from organizational, social and technical perspective. It clearly shows how information is facilitated within a healthcare organization, reducing duplicated data entry, and guiding the future technological implementation.

HMEF: framework to evaluate merging of Higher Education Institutions – application of Enterprise Architecture

Mergers of Higher Education Institutions (HEIs) are organisational processes requiring tremendous amount of resources, in terms of time, work, and money. A number of mergers have been seen on previous years and more are to come. Several studies on mergers have been conducted, revealing some crucial factors that affect the success of mergers. Based on literature review on these studies, factors are: the initiator of merger, a reason for merger, geographical distance of merging institutions, organisational culture, the extend of overlapping course portfolio, and Quality Assurance Systems (QASs). Usually these kind of factors are not considered on mergers, but focus is on financial matters. In this paper, a framework (HMEF) for evaluating merging of HEIs is introduced. HMEF is based on Enterprise Architecture (EA), focusing on factors found to be affecting the success of mergers. By using HMEF, HEIs can focus on matters that crucial for merging.

Taxonomy of purpose of Enterprise Architecture

Initial phase of all Enterprise Architecture (EA) initiatives is important. One of the most crucial tasks in that phase is to sell EA to the top management by explaining its purpose. In this paper, by using semiotic framework we show that there is a clear gap between the definition of EA and its purpose. Contribution of this paper is a taxonomy that expands knowledge of pragmatics of EA, and that can be used as a tool for explaining the purpose of EA. Grounded theory is used to form the taxonomy. Data is collected from a discussion group used by EA practitioners. Results indicate that the purpose of EA is to meet organisations‟ stakeholder‟s goals and to create value to organisation. Results are in line with current literature. Most interesting result is that EA practitioners seem to realise that technical solutions are not the purpose of EA, but means for fulfilling it.

Measuring Enterprise Architecture success: a tentative model for measuring success

Interest towards Enterprise Architecture (EA) has been increasing during the last few years. EA has been found to be a crucial aspect of business survival, and thus the importance of EA implementation success is also crucial. Current literature does not have a tool to be used to measure the success of EA implementation. In this paper, a tentative model for measuring success is presented and empirically validated in EA context. Results show that the success of EA implementation can be measured indirectly by measuring the achievement of the objectives set for the implementation. Results also imply that achieving individual's objectives do not necessarily mean that organisation's objectives are achieved. The presented Success Measurement Model can be used as basis for developing measurement metrics.